REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
PE-Vio770 anti-human CXCR5	Miltenyi Biotec	Cat# 130-117-358; RRID:AB_2733205
PE anti-human PD-1	Miltenyi Biotec	Cat# 130-117-384; RRID:AB_2727929
Percp-Vio770 anti-human CD3	Miltenyi Biotec	Cat# 130-113-141; RRID:AB_2725969
APC anti-human CD19	Miltenyi Biotec	Cat# 130-110-250; RRID:AB_2655809
Vioblue anti-human ICOS	Miltenyi Biotec	Cat# 130-100-737; RRID:AB_2656918
PE-Vio770 anti-human CD38	Miltenyi Biotec	Cat# 130-099-151; RRID:AB_2660384
Vioblue anti-human CD40L	Miltenyi Biotec	Cat# 130-109-470; RRID:AB_2655266
APC-Vio770 anti-human CD4	Miltenyi Biotec	Cat# 130-113-223; RRID:AB_2726034
FITC anti-human IFNγ	Miltenyi Biotec	Cat# 130-113-497; RRID:AB_2733587
APC anti-human IL-21	Miltenyi Biotec	Cat# 130-117-421; RRID:AB_2727941
PE-Vio615 anti-human CD45RA	Miltenyi Biotec	Cat# 130-118-789; RRID:AB_2732979
PE anti-human CD27	Miltenyi Biotec	Cat# 130-113-640; RRID:AB_2726194
APC anti-human Bcl6	BD Bioscience	Cat# 561525; RRID:AB_10898007
Vio Bright FITC anti-human CXCR3	Miltenyi Biotec	Cat# 130-118-673; RRID:AB_2734057
FITC KC57 (anti-p24)	Beckman Coulter	Cat# 6604665; RRID:AB_1575987
Pure anti-human CCR5	Miltenyi Biotec	Cat# 130-122-313; RRID:AB_2801894
Pure anti-human CD56	Miltenyi Biotec	Cat# 130-108-016; RRID:AB_2658728
Pure anti-human CCR7	Miltenyi Biotec	Cat# 130-122-300; RRID:AB_2801881
Pure anti-human CD62L (Custom Reagent Cell Analysis)	Miltenyi Biotec	Cat# 130-113-625; RRID:AB_2733829
Pure anti-human IL-1R2 (Custom Reagent Cell Analysis)	Miltenyi Biotec	Cat# 130-126-459
Purified anti-human IL-1R1 Polyclonal Ab	Bio-techne	Cat# AF269; RRID:AB_355286
Purified anti-human BTLA Polyclonal Ab	Bio-techne	Cat# AF3354; RRID:AB_2065766
Anti-Human Ki-67 (B56)- 172Yb	Fluidigm	Cat# 3172024B; RRID:AB_2858243
Anti-Human CD152/CTLA-4 (14D3)-170Er	Fluidigm	Cat# 3170005B; RRID:AB_2858238
Anti-Human CD28 (CD28.2)-160Gd	Fluidigm	Cat# 3160003B; RRID:AB_2868400
Anti-Human CD134/OX40 (ACT35)-158Gd	Fluidigm	Cat# 3158012B
Anti-CD278/ICOS (C398.4A)-151Eu	Fluidigm	Cat# 3151020B
Anti-Human CD154/CD40L (24-31)-168Er	Fluidigm	Cat# 3168006B
Anti-Human CD196/CCR6 (11A9)-141Pr	Fluidigm	Cat# 3141014A
Anti-Human CD183/CXCR3 (G025H7)-156Gd	Fluidigm	Cat# 3156004B; RRID:AB_2687646
Anti-Human CD279/PD-1 (EH12.2H7)-155Gd	Fluidigm	Cat# 3155009B; RRID:AB_2811087
Anti-Human CD185/CXCR5 (RF8B2)-171Yb	Fluidigm	Cat# 3171014B; RRID:AB_2858239
Anti-Human HLA-DR (L243)-173Yb	Fluidigm	Cat# 3173005B; RRID:AB_2810248
Anti-Human CD38 (HIT2)- 144Nd	Fluidigm	Cat# 3144014B; RRID:AB_2687640
Anti-Human CD127/IL-7Ra (A019D5)-165Ho	Fluidigm	Cat# 3165008B; RRID:AB_2868401
Anti-Human CD27 (L128)- 162Dy	Fluidigm	Cat# 3162009B; RRID:AB_2756422
Anti-Human CD95/Fas (DX2)-152Sm	Fluidigm	Cat# 3152017B
Anti-Human CD8 (RPA-T8)- 146Nd	Fluidigm	Cat# 3146001; RRID:AB_2687641
Anti-Human CD19 (HIB19)- 142Nd	Fluidigm	Cat# 3142001; RRID:AB_2651155
Anti-Human CD4 (RPA-T4)- 145Nd	Fluidigm	Cat# 3145001; RRID:AB_2661789
Anti-Human CD45RO (UCHL1)-164Dy	Fluidigm	Cat# 3164007B; RRID:AB_2811092
Anti-Human CD45 (HI30)- Y89	Fluidigm	Cat# 3089003; RRID:AB_2661851
Anti-Human CD45RA (HI100)-143Nd	Fluidigm	Cat# 3143006B; RRID:AB_2651156
Anti-Human CD25 (2A3)- 149Sm	Fluidigm	Cat# 3149010B; RRID:AB_2756416
Anti-Human FoxP3 (259D/ C7)-159Tb	Fluidigm	Cat# 3159028A; RRID:AB_2811088
Anti-Human CD184/CXCR4 (12G5)-175Lu	Fluidigm	Cat# 3175001B
Bacterial and virus strains
HIV-1 R5 strain YU2b	Cardinaud et al. (2017)	N/A
Biological samples
PBMC	Etablissement français du sang	N/A
Spleens	Biomedecine Agency	N/A
Chemicals, peptides, and recombinant proteins
Recombinant human Activin A, premium grade	Miltenyi	Cat# 130-115-010
Recombinant human IL-7, premium grade	Miltenyi	Cat# 130-095-363
Recombinant IL-12, premium grade	Miltenyi	Cat# 130-096-798
CytoStim™, human	Miltenyi	Cat# 130-092-173
Cell-IDTM Intercalator-Rh	Fluidigm	Cat# 201103B
Cell-IDTM Cisplatin-198Pt	Fluidigm	Cat# 201198
Cell-IDTM Intercalator-Ir	Fluidigm	Cat# 201192B
EQ Four Element Calibration Beads	Fluidigm	Cat# 201078
LIVE/DEAD™ Fixable Aqua	Thermofisher	Cat# L34957
Fixable Viability Dye eFluor™ 780	Thermofisher	Cat# 65-0865-14
Cell Trace Violet	Thermofisher	Cat# C34557
PMA	Sigma-Aldrich	Cat# P1585
Ionomycin	Sigma-Aldrich	Cat# I9657
Brefeldin A	Sigma-Aldrich	Cat# B6542
DNase	Sigma-Aldrich	Cat# 10104159001
Fc Block	Miltenyi	Cat# 130-059-901
Critical commercial assays
BD Cytofix/Cytoperrm Kit	BD Biosciences	Cat# 554714
Transcription Factor Buffer Set	BD Biosciences	Cat# 562574
Maxpar® X8 Antibody Labeling Kit, 150Nd—4 Rxn	Fluidigm	Cat# 201150A
Maxpar® X8 Antibody Labeling Kit, 174Yb—4 Rxn	Fluidigm	Cat# 201174A
Maxpar® X8 Antibody Labeling Kit, 148Nd—4 Rxn	Fluidigm	Cat# 201148A
Maxpar® X8 Antibody Labeling Kit, 153Eu—4 Rxn	Fluidigm	Cat# 201153A
Maxpar® X8 Antibody Labeling Kit, 169Tm—4 Rxn	Fluidigm	Cat# 201169A
Maxpar® X8 Antibody Labeling Kit, 166Er—4 Rxn	Fluidigm	Cat# 201166A
Maxpar® X8 Antibody Labeling Kit, 154Sm—4 Rxn	Fluidigm	Cat# 201154A
Maxpar® X8 Antibody Labeling Kit, 176Yb—4 Rxn	Fluidigm	Cat# 201176A
Maxpar® X8 Antibody Labeling Kit, 147Sm—4 Rxn	Fluidigm	Cat# 201147A
Calcium Phosphate Transfection Kit	Sigma-Aldrich	Cat# CAPHOS-1KT
RNeasy Mini Kit	Qiagen	Cat# 74106
Cytokine 7-Plex Human ProcartaPlex™ Panel 1C	Thermo Fisher Scientific	Cat# EPX070-10010-901; RRID:AB_2576087
Experimental models: Cell lines
293T	ATCC	Cat# CRL-3216
Software and algorithms
BD FACSDiva Software	BD Biosciences	http://www.bdbiosciences.com/instruments/software/facsdiva/index.jsp BD FACSDiva Software (RRID:SCR_001456)
FlowJo v10	FlowJo LLC, USA	FlowJo (RRID:SCR_008520)
GraphPad Prism 6	GraphPad	http://www.graphpad.com/GraphPad Prism (RRID:SCR_002798)
R software	R software	http://www.r-project.org/R Project for Statistical Computing (RRID:SCR_001905)
UMAP algorithm	McInnes et al., 2018	https://github.com/lmcinnes/umap Umap (RRID:SCR_018217)
“CytoTree” R package	Dai et al. (2021)	https://github.com/JhuangLab/CytoTree
Cutadapt	Martin (2011)	http://code.google.com/p/cutadapt/cutadapt (RRID:SCR_011841)
Salmon	Patro et al. (2017)	https://combine-lab.github.io/salmon/Salmon (RRID:SCR_017036)
DESeq2	Love et al. (2014)	https://bioconductor.org/packages/release/bioc/html/DESeq2.html DESeq2 (RRID:SCR_015687)
EnrichR	Chen et al. (2013)	http://amp.pharm.mssm.edu/Enrichr/Enrichr (RRID:SCR_001575)
Deposited data
https://doi.org/10.17632/zs4y45ctdw.1